However I am not sure how you plan on using Galaxy's API without being interested in the tools that will perform the analysis steps. Galaxy itself is an engine to run tools. Without the tools you can't do much.

Hello, The solution here is most likely a Workflow that utilizes the tool that Bjoern mentions. Create the Workflow on your server (once the tool is loaded, or you wrap/load your own tool that perform the read->transcript mapping), add in the other tools/steps needed (input reference data, mapping transcript to gene names/IDs from the source you want to use, etc.). Then that Workflow can be executed through the API. Thanks, Jen, Galaxy team